1010# #' @export
1111create_codecheck_files <- function () {
1212 if (file.exists(" codecheck.yml"
13- stop(" codecheck.yml already exists, so stopping."
14- else
13+ warning(" codecheck.yml already exists, so not overwriting it."
14+ " See the template file at "
15+ system.file(" extdata" " templates/codecheck.yml" package = " codecheck"
16+ " for required metadata and examples."
17+ else
18+ copy_codecheck_yaml_template()
19+
1520 if (dir.exists(" codecheck"
1621 stop(" codecheck folder exists, so stopping."
17- copy_codecheck_yaml_template()
18- copy_codecheck_report_template()
22+ else
23+ copy_codecheck_report_template()
1924}
2025
2126copy_codecheck_yaml_template <- function (target = " ."
2227 templates <- system.file(" extdata" " templates" package = " codecheck"
2328 file.copy(file.path(templates , " codecheck.yml" target )
29+ cat(" Created codecheck.yml file at " target , " \n "
2430}
2531
2632copy_codecheck_report_template <- function (target = " ."
2733 templates <- system.file(" extdata" " templates" package = " codecheck"
2834 file.copy(file.path(templates , " codecheck" target , recursive = TRUE )
35+ cat(" Created codecheck report files at " target , " :" " codecheck" " \n "
2936}
3037
31-
32-
3338# #' Return the metadata for the codecheck project in root folder of project
3439# #'
3540# #' @title Return the metadata for the codecheck project in root folder of project
36- # #' @param root Path to the root folder of the project.
41+ # #' @param root Path to the root folder of the project, defaults to current working directory
3742# #' @return A list containing the metadata found in the codecheck.yml file
3843# #' @author Stephen Eglen
3944# #' @importFrom yaml read_yaml
4045# #' @export
41- codecheck_metadata <- function (root ) {
42- read_yaml( file.path(root , " codecheck.yml"
46+ codecheck_metadata <- function (root = getwd() ) {
47+ read_yaml(file.path(root , " codecheck.yml"
4348}
4449
45-
4650# #' Copy manifest files into the root/codecheck/outputs folder; return manifest.
4751# #'
4852# #' The metadata should specify the manifest -- the files to copy into the
@@ -51,17 +55,19 @@ codecheck_metadata <- function(root) {
5155# #' If KEEP_FULL_PATH is TRUE, we keep the full path for the output files.
5256# #' This is useful when there are two output files with the same name in
5357# #' different folders, e.g. expt1/out.pdf and expt2/out.pdf
54-
58+ # #'
5559# #' @title Copy files from manifest into the codecheck folder and summarise.
56- # #' @param root - Path to the root folder of the proejct .
60+ # #' @param root - Path to the root folder of the project .
5761# #' @param metadata - the codecheck metadata list.
5862# #' @param dest_dir - folder where outputs are to be copied to (codecheck/outputs)
5963# #' @param keep_full_path - TRUE to keep relative pathname of figures.
64+ # #' @param overwrite - TRUE to overwrite the output files even if they already exist
6065# #' @return A dataframe containing one row per manifest file.
6166# #' @author Stephen Eglen
6267# #' @export
6368copy_manifest_files <- function (root , metadata , dest_dir ,
64- keep_full_path = FALSE ) {
69+ keep_full_path = FALSE ,
70+ overwrite = FALSE ) {
6571 manifest = metadata $ manifest
6672 outputs = sapply(manifest , function (x ) x $ file )
6773 src_files = file.path(root , outputs )
@@ -83,8 +89,10 @@ copy_manifest_files <- function(root, metadata, dest_dir,
8389 dir.create(dir , recursive = TRUE )
8490 }
8591 }
86- file.copy(src_files , dest_files , overwrite = TRUE )
87- dest_files
92+
93+ if (overwrite ) message(" Overwriting output files: " dest_files ))
94+ file.copy(src_files , dest_files , overwrite = overwrite )
95+
8896 manifest_df = data.frame (output = outputs ,
8997 comment = sapply(manifest , function (x ) x $ comment ),
9098 dest = dest_files ,
@@ -93,11 +101,29 @@ copy_manifest_files <- function(root, metadata, dest_dir,
93101 manifest_df
94102}
95103
96-
97-
104+ # #' List manifest.
105+ # #'
106+ # #' @title Summarise manifest files.
107+ # #' @param root - Path to the root folder of the project.
108+ # #' @param metadata - the codecheck metadata list.
109+ # #' @param check_dir - folder where outputs have been copied to (codecheck/outputs)
110+ # #' @return A dataframe containing one row per manifest file.
111+ # #' @author Daniel Nüst
112+ # #' @export
113+ list_manifest_files <- function (root , metadata , check_dir ) {
114+ manifest = metadata $ manifest
115+ outputs = sapply(manifest , function (x ) x $ file )
116+ dest_files = file.path(check_dir , basename(outputs ))
117+ manifest_df = data.frame (output = outputs ,
118+ comment = sapply(manifest , function (x ) x $ comment ),
119+ dest = dest_files ,
120+ size = file.size(dest_files ),
121+ stringsAsFactors = FALSE )
122+ manifest_df
123+ }
98124
99125# # latex summary of metadata
100-
126+ # #
101127# # https://daringfireball.net/2010/07/improved_regex_for_matching_urls
102128# # To use the URL in R, I had to escape the \ characters and " -- this version
103129# # does not work:
@@ -117,7 +143,7 @@ copy_manifest_files <- function(root, metadata, dest_dir,
117143# #' Wrap URL for LaTeX
118144# #'
119145# #' @param x - A string that may contain URLs that should be hyperlinked.
120- # #' @return A string with the passed url as a latex `\url{}`
146+ # #' @return A string with the passed URL as a latex `\url{http://the.url }`
121147# #' @author Stephen Eglen
122148# #' @importFrom stringr str_replace_all
123149as_latex_url <- function (x ) {
@@ -265,7 +291,7 @@ create_zenodo_record <- function(zen) {
265291 this_doi = myrec $ metadata $ prereserve_doi $ doi
266292 cat(" The following URL is your Zenodo DOI.\n "
267293 cat(" Please add this to codecheck.yml in report: field\n "
268- print(this_doi )
294+ print(paste0( " https://doi.org/ " , this_doi ) )
269295 cat(" Remember to reload the yaml file after editing it.\n "
270296 get_zenodo_record(this_doi )
271297}
0 commit comments